Multiple sequence alignment - TraesCS2D01G528200

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2D01G528200 chr2D 100.000 3667 0 0 1 3667 615590606 615594272 0.000000e+00 6772
1 TraesCS2D01G528200 chr2D 90.426 94 8 1 2637 2729 615612695 615612788 4.970000e-24 122
2 TraesCS2D01G528200 chr2A 88.866 2910 168 66 1 2828 745654621 745657456 0.000000e+00 3435
3 TraesCS2D01G528200 chr2A 84.887 311 29 7 2527 2828 745659440 745659741 7.700000e-77 298
4 TraesCS2D01G528200 chr2B 92.877 2120 91 24 700 2772 750001658 750003764 0.000000e+00 3024
5 TraesCS2D01G528200 chr2B 84.938 644 56 19 1 627 750001046 750001665 6.730000e-172 614
6 TraesCS2D01G528200 chr5A 93.506 616 34 4 2827 3438 601824678 601824065 0.000000e+00 911
7 TraesCS2D01G528200 chrUn 93.019 616 37 4 2827 3438 296977272 296977885 0.000000e+00 894
8 TraesCS2D01G528200 chr6B 92.869 617 38 4 2826 3438 643414144 643413530 0.000000e+00 891
9 TraesCS2D01G528200 chr6B 88.626 211 18 2 1145 1355 703169316 703169112 6.080000e-63 252
10 TraesCS2D01G528200 chr6B 76.522 345 81 0 2161 2505 703166392 703166048 4.830000e-44 189
11 TraesCS2D01G528200 chr5B 85.665 872 64 29 2828 3666 138848090 138848933 0.000000e+00 861
12 TraesCS2D01G528200 chr7D 88.732 426 42 6 2827 3248 49208524 49208947 1.950000e-142 516
13 TraesCS2D01G528200 chr7D 83.032 442 47 8 2827 3261 12149536 12149116 3.460000e-100 375
14 TraesCS2D01G528200 chr4A 88.471 425 44 5 2827 3248 725894798 725895220 3.270000e-140 508
15 TraesCS2D01G528200 chr1B 83.575 414 53 12 2828 3236 19224397 19223994 1.240000e-99 374
16 TraesCS2D01G528200 chr6A 77.660 376 80 3 2156 2528 608091059 608090685 3.680000e-55 226
17 TraesCS2D01G528200 chr6D 77.714 350 78 0 2156 2505 461416000 461415651 7.980000e-52 215


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G528200 chr2D 615590606 615594272 3666 False 6772.0 6772 100.0000 1 3667 1 chr2D.!!$F1 3666
1 TraesCS2D01G528200 chr2A 745654621 745659741 5120 False 1866.5 3435 86.8765 1 2828 2 chr2A.!!$F1 2827
2 TraesCS2D01G528200 chr2B 750001046 750003764 2718 False 1819.0 3024 88.9075 1 2772 2 chr2B.!!$F1 2771
3 TraesCS2D01G528200 chr5A 601824065 601824678 613 True 911.0 911 93.5060 2827 3438 1 chr5A.!!$R1 611
4 TraesCS2D01G528200 chrUn 296977272 296977885 613 False 894.0 894 93.0190 2827 3438 1 chrUn.!!$F1 611
5 TraesCS2D01G528200 chr6B 643413530 643414144 614 True 891.0 891 92.8690 2826 3438 1 chr6B.!!$R1 612
6 TraesCS2D01G528200 chr6B 703166048 703169316 3268 True 220.5 252 82.5740 1145 2505 2 chr6B.!!$R2 1360
7 TraesCS2D01G528200 chr5B 138848090 138848933 843 False 861.0 861 85.6650 2828 3666 1 chr5B.!!$F1 838

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
750 795 0.035152 TCATCCACCATGTGCCTCAC 60.035 55.0 0.0 0.0 33.66 3.51 F
1835 2394 1.012841 GCTTGGATCGAAGCCTGAAG 58.987 55.0 26.8 0.0 42.23 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1968 2617 0.036952 CCATGCCGAAGTCTGACAGT 60.037 55.0 10.88 0.0 0.0 3.55 R
3415 7806 0.700564 CATACCCTGGCCCTGCATAT 59.299 55.0 0.00 0.0 0.0 1.78 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 44 1.203313 AGCAGGTGTCTTCTTCCCCTA 60.203 52.381 0.00 0.00 0.00 3.53
36 45 1.840635 GCAGGTGTCTTCTTCCCCTAT 59.159 52.381 0.00 0.00 0.00 2.57
37 46 2.158885 GCAGGTGTCTTCTTCCCCTATC 60.159 54.545 0.00 0.00 0.00 2.08
38 47 2.436173 CAGGTGTCTTCTTCCCCTATCC 59.564 54.545 0.00 0.00 0.00 2.59
43 52 3.311327 TGTCTTCTTCCCCTATCCATCCA 60.311 47.826 0.00 0.00 0.00 3.41
141 159 0.672711 GCCGAGGAACCGTAAAAGCT 60.673 55.000 0.00 0.00 0.00 3.74
149 167 3.122445 GGAACCGTAAAAGCTACGACTTG 59.878 47.826 9.06 0.00 42.94 3.16
201 223 2.046892 CAGGCCGGTCACCTCAAG 60.047 66.667 9.71 0.00 34.42 3.02
202 224 2.526873 AGGCCGGTCACCTCAAGT 60.527 61.111 9.71 0.00 28.76 3.16
214 237 0.551396 CCTCAAGTAACCCCATCCCC 59.449 60.000 0.00 0.00 0.00 4.81
216 239 1.490910 CTCAAGTAACCCCATCCCCTC 59.509 57.143 0.00 0.00 0.00 4.30
246 269 0.541392 CACCCCGTTGGATCATCAGA 59.459 55.000 0.00 0.00 38.00 3.27
249 272 0.467384 CCCGTTGGATCATCAGAGCT 59.533 55.000 0.00 0.00 0.00 4.09
290 317 7.303998 AGGTAATCGACTATACGCTGTTAATC 58.696 38.462 0.00 0.00 0.00 1.75
322 349 1.303561 TGCTCCGGCAAGCTGATTT 60.304 52.632 15.49 0.00 46.36 2.17
323 350 0.895100 TGCTCCGGCAAGCTGATTTT 60.895 50.000 15.49 0.00 46.36 1.82
325 352 0.883833 CTCCGGCAAGCTGATTTTGT 59.116 50.000 0.00 0.00 0.00 2.83
343 370 1.754226 TGTTGTCCCAGCTTTGGTTTC 59.246 47.619 0.00 0.00 0.00 2.78
367 394 0.325671 GACATGGAGGGAGGGAGTGA 60.326 60.000 0.00 0.00 0.00 3.41
368 395 0.119155 ACATGGAGGGAGGGAGTGAA 59.881 55.000 0.00 0.00 0.00 3.18
369 396 1.289160 CATGGAGGGAGGGAGTGAAA 58.711 55.000 0.00 0.00 0.00 2.69
370 397 1.211457 CATGGAGGGAGGGAGTGAAAG 59.789 57.143 0.00 0.00 0.00 2.62
371 398 0.193574 TGGAGGGAGGGAGTGAAAGT 59.806 55.000 0.00 0.00 0.00 2.66
372 399 0.615850 GGAGGGAGGGAGTGAAAGTG 59.384 60.000 0.00 0.00 0.00 3.16
373 400 1.645710 GAGGGAGGGAGTGAAAGTGA 58.354 55.000 0.00 0.00 0.00 3.41
374 401 1.978580 GAGGGAGGGAGTGAAAGTGAA 59.021 52.381 0.00 0.00 0.00 3.18
422 450 1.633852 CCGCTGCTCTGCTCTGTTTC 61.634 60.000 0.00 0.00 0.00 2.78
464 492 2.101249 CCTCTGCTTCTTCTGCTAGGAG 59.899 54.545 4.60 4.60 36.84 3.69
465 493 1.480137 TCTGCTTCTTCTGCTAGGAGC 59.520 52.381 6.35 7.22 45.40 4.70
466 494 1.481772 CTGCTTCTTCTGCTAGGAGCT 59.518 52.381 6.35 0.00 45.40 4.09
469 497 2.955660 GCTTCTTCTGCTAGGAGCTAGA 59.044 50.000 6.35 8.86 42.47 2.43
478 506 2.691545 GCTAGGAGCTAGAAAGGGAGGT 60.692 54.545 0.00 0.00 38.45 3.85
529 564 2.357009 GCTCAATCCGATCTGCAATTGT 59.643 45.455 7.40 0.00 32.31 2.71
536 575 5.022282 TCCGATCTGCAATTGTATCTGAA 57.978 39.130 7.40 0.00 0.00 3.02
537 576 4.811024 TCCGATCTGCAATTGTATCTGAAC 59.189 41.667 7.40 0.00 0.00 3.18
538 577 4.024556 CCGATCTGCAATTGTATCTGAACC 60.025 45.833 7.40 0.00 0.00 3.62
539 578 4.813161 CGATCTGCAATTGTATCTGAACCT 59.187 41.667 7.40 0.00 0.00 3.50
601 640 6.708285 GGGGATTTATTCACCGTGTATAGAT 58.292 40.000 0.00 0.00 38.43 1.98
639 679 0.896940 CCTTGCCTGCCTGTGTTCAT 60.897 55.000 0.00 0.00 0.00 2.57
665 705 0.108963 CGTCCCTCTCCCTAGATCGT 59.891 60.000 0.00 0.00 0.00 3.73
680 720 0.107897 ATCGTGCCCTAAATCGTGCA 60.108 50.000 0.00 0.00 0.00 4.57
712 752 0.545309 TGTACCTCCTTGCCTGCTCT 60.545 55.000 0.00 0.00 0.00 4.09
746 791 1.679680 CATCTTCATCCACCATGTGCC 59.320 52.381 0.00 0.00 33.66 5.01
748 793 1.065199 TCTTCATCCACCATGTGCCTC 60.065 52.381 0.00 0.00 33.66 4.70
749 794 0.697658 TTCATCCACCATGTGCCTCA 59.302 50.000 0.00 0.00 33.66 3.86
750 795 0.035152 TCATCCACCATGTGCCTCAC 60.035 55.000 0.00 0.00 33.66 3.51
812 877 5.197451 TGATGGTGTTTGTTGGAGTAAACT 58.803 37.500 0.00 0.00 37.60 2.66
845 910 2.224305 CCTGGCGGCTAAGCTACTTTAT 60.224 50.000 11.43 0.00 37.29 1.40
973 1067 7.246674 TCATCAGGTAAACAAATCGATTAGC 57.753 36.000 11.83 5.01 32.25 3.09
1320 1417 4.598894 CTCATGCTCGGCGAGGGG 62.599 72.222 35.03 17.31 0.00 4.79
1357 1463 4.424711 GGGGCGCCATCAAGGTCA 62.425 66.667 30.85 0.00 40.61 4.02
1460 1571 8.815565 AGATACATACAGATATACTCCACCAG 57.184 38.462 0.00 0.00 0.00 4.00
1835 2394 1.012841 GCTTGGATCGAAGCCTGAAG 58.987 55.000 26.80 0.00 42.23 3.02
1938 2587 1.337823 CGGGACCTGAAGACGTCAAAT 60.338 52.381 19.50 2.96 35.22 2.32
1941 2590 4.202080 CGGGACCTGAAGACGTCAAATATA 60.202 45.833 19.50 0.00 35.22 0.86
1942 2591 5.509163 CGGGACCTGAAGACGTCAAATATAT 60.509 44.000 19.50 0.00 35.22 0.86
1968 2617 0.400213 ATGAGGACTGGAACGCCAAA 59.600 50.000 0.00 0.00 45.41 3.28
2036 2685 1.007336 CACGTCTCCACAGCGGTAAC 61.007 60.000 0.00 0.00 35.57 2.50
2134 3691 8.589335 AGTACGAAATGGATTATGACATGTAC 57.411 34.615 0.00 0.00 30.41 2.90
2267 4342 0.393944 TCTACGAGCTCATCACGGGT 60.394 55.000 15.40 3.93 32.98 5.28
2654 4738 0.701147 CTGGAAGAGGAAAAGGGCCT 59.299 55.000 0.00 0.00 38.81 5.19
2668 4752 0.761187 GGGCCTCTCATGTGCTGATA 59.239 55.000 0.84 0.00 32.10 2.15
2673 4757 3.799574 GCCTCTCATGTGCTGATACTGAG 60.800 52.174 0.00 0.00 35.71 3.35
2688 4772 7.659390 GCTGATACTGAGGCTAGTTTAATTCAT 59.341 37.037 0.00 0.00 32.19 2.57
2708 4792 9.740239 AATTCATGTGATTGATTAGATTTTCGG 57.260 29.630 0.00 0.00 0.00 4.30
2717 7081 6.360370 TGATTAGATTTTCGGGGATCCTAG 57.640 41.667 12.58 6.18 0.00 3.02
2741 7105 4.850347 AATCCTAGTACGGCAGTATGTC 57.150 45.455 0.00 0.00 39.31 3.06
2757 7121 2.208132 TGTCTGTTGGTGGTGTTGTT 57.792 45.000 0.00 0.00 0.00 2.83
2758 7122 2.088423 TGTCTGTTGGTGGTGTTGTTC 58.912 47.619 0.00 0.00 0.00 3.18
2775 7139 5.471116 TGTTGTTCTGAGTGATCAATTCCAG 59.529 40.000 0.00 0.79 36.93 3.86
2777 7141 3.272574 TCTGAGTGATCAATTCCAGCC 57.727 47.619 0.00 0.00 0.00 4.85
2792 7156 2.092049 TCCAGCCGGAAGAGTCATAGTA 60.092 50.000 5.05 0.00 38.83 1.82
2799 7163 4.294232 CGGAAGAGTCATAGTATGCAGTG 58.706 47.826 5.18 0.00 0.00 3.66
2800 7164 4.202060 CGGAAGAGTCATAGTATGCAGTGT 60.202 45.833 5.18 0.00 0.00 3.55
2812 7178 2.049888 TGCAGTGTCAATTGTGTGGA 57.950 45.000 5.13 0.00 0.00 4.02
2844 7210 4.262079 GGCTATACTAGAACATGAAGGCGT 60.262 45.833 0.00 0.00 0.00 5.68
2851 7217 1.444119 AACATGAAGGCGTGCGTTGT 61.444 50.000 4.32 0.00 34.29 3.32
2853 7219 1.596752 ATGAAGGCGTGCGTTGTCA 60.597 52.632 4.32 0.00 0.00 3.58
2855 7221 2.512745 AAGGCGTGCGTTGTCACA 60.513 55.556 0.00 0.00 36.80 3.58
2867 7233 1.265905 GTTGTCACACCCGTCCATTTC 59.734 52.381 0.00 0.00 0.00 2.17
2941 7307 2.203195 AACAAGTCGGCAGCTGCA 60.203 55.556 37.63 18.09 44.36 4.41
3080 7446 5.566032 CGCCCGACCTCAGTTTATATATTCA 60.566 44.000 0.00 0.00 0.00 2.57
3211 7598 9.872721 TCCATATACGAACAGTTGTTAATTACA 57.127 29.630 0.00 0.00 38.56 2.41
3228 7615 9.868277 GTTAATTACAAATGGGTCATGAATTCA 57.132 29.630 11.26 11.26 0.00 2.57
3262 7650 7.079182 TCAACACTAAATTCGTCAGTTTTGT 57.921 32.000 0.00 0.00 33.66 2.83
3272 7660 4.976987 TCGTCAGTTTTGTTTTTCAGGTC 58.023 39.130 0.00 0.00 0.00 3.85
3333 7721 8.653036 AGGGTGTTCCTATGTACTCTATATTC 57.347 38.462 0.00 0.00 45.98 1.75
3404 7795 3.373130 TCACATCACCGAGTACTAACGAG 59.627 47.826 5.60 0.00 0.00 4.18
3414 7805 5.335191 CCGAGTACTAACGAGTTACCAAAGT 60.335 44.000 5.60 0.00 37.10 2.66
3415 7806 6.128282 CCGAGTACTAACGAGTTACCAAAGTA 60.128 42.308 5.60 0.00 37.10 2.24
3446 7839 3.744530 GCCAGGGTATGCGATAGAAAACT 60.745 47.826 0.00 0.00 39.76 2.66
3462 7855 8.870075 ATAGAAAACTGATTAAGAAAGGCAGT 57.130 30.769 0.00 0.00 41.19 4.40
3494 7887 1.322442 AGAGTTCACCAAAAGCAGGC 58.678 50.000 0.00 0.00 0.00 4.85
3498 7891 1.733402 TTCACCAAAAGCAGGCCACG 61.733 55.000 5.01 0.00 0.00 4.94
3519 7916 2.165030 GCAACATAGCTTGCAGGACATT 59.835 45.455 0.00 0.00 45.07 2.71
3520 7917 3.733077 GCAACATAGCTTGCAGGACATTC 60.733 47.826 0.00 0.00 45.07 2.67
3521 7918 3.354948 ACATAGCTTGCAGGACATTCA 57.645 42.857 0.00 0.00 0.00 2.57
3522 7919 3.276857 ACATAGCTTGCAGGACATTCAG 58.723 45.455 0.00 0.00 0.00 3.02
3568 7965 2.762745 TCAACTTCGAGGTAGCCAAAC 58.237 47.619 0.00 0.00 0.00 2.93
3570 7967 2.737252 CAACTTCGAGGTAGCCAAACTC 59.263 50.000 0.00 0.00 0.00 3.01
3572 7969 2.567615 ACTTCGAGGTAGCCAAACTCAT 59.432 45.455 0.00 0.00 0.00 2.90
3573 7970 3.008049 ACTTCGAGGTAGCCAAACTCATT 59.992 43.478 0.00 0.00 0.00 2.57
3574 7971 3.247006 TCGAGGTAGCCAAACTCATTC 57.753 47.619 2.92 0.00 0.00 2.67
3575 7972 2.093658 TCGAGGTAGCCAAACTCATTCC 60.094 50.000 2.92 0.00 0.00 3.01
3576 7973 2.644676 GAGGTAGCCAAACTCATTCCC 58.355 52.381 0.00 0.00 0.00 3.97
3578 7975 1.005450 GGTAGCCAAACTCATTCCCCA 59.995 52.381 0.00 0.00 0.00 4.96
3579 7976 2.556559 GGTAGCCAAACTCATTCCCCAA 60.557 50.000 0.00 0.00 0.00 4.12
3631 8028 7.177184 TGCAGGAGTCCATATATGCAAAATAT 58.823 34.615 18.00 0.00 40.43 1.28
3644 8042 5.181690 TGCAAAATATAATGAGTTCGCCC 57.818 39.130 0.00 0.00 0.00 6.13
3658 8056 4.133796 GCCCAAATGAGCACCGGC 62.134 66.667 0.00 0.00 41.61 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 44 2.068977 GGAGGAAAGGGATGGATGGAT 58.931 52.381 0.00 0.00 0.00 3.41
36 45 1.522900 GGAGGAAAGGGATGGATGGA 58.477 55.000 0.00 0.00 0.00 3.41
37 46 0.480252 GGGAGGAAAGGGATGGATGG 59.520 60.000 0.00 0.00 0.00 3.51
38 47 1.423161 GAGGGAGGAAAGGGATGGATG 59.577 57.143 0.00 0.00 0.00 3.51
43 52 1.299939 GTTGGAGGGAGGAAAGGGAT 58.700 55.000 0.00 0.00 0.00 3.85
149 167 1.000496 AGACGAAGGTGGACGAAGAAC 60.000 52.381 0.00 0.00 0.00 3.01
197 219 1.591768 GAGGGGATGGGGTTACTTGA 58.408 55.000 0.00 0.00 0.00 3.02
201 223 0.551396 CAAGGAGGGGATGGGGTTAC 59.449 60.000 0.00 0.00 0.00 2.50
202 224 1.286305 GCAAGGAGGGGATGGGGTTA 61.286 60.000 0.00 0.00 0.00 2.85
214 237 2.045536 GGGTGAGGCAGCAAGGAG 60.046 66.667 0.00 0.00 33.07 3.69
290 317 1.466167 CGGAGCAAGATCAACCAACTG 59.534 52.381 0.00 0.00 0.00 3.16
315 342 1.615392 AGCTGGGACAACAAAATCAGC 59.385 47.619 0.00 0.00 45.37 4.26
343 370 1.565759 TCCCTCCCTCCATGTCAAATG 59.434 52.381 0.00 0.00 0.00 2.32
367 394 3.031013 CAGGGGGTTTCACTTTCACTTT 58.969 45.455 0.00 0.00 0.00 2.66
368 395 2.666317 CAGGGGGTTTCACTTTCACTT 58.334 47.619 0.00 0.00 0.00 3.16
369 396 1.754201 GCAGGGGGTTTCACTTTCACT 60.754 52.381 0.00 0.00 0.00 3.41
370 397 0.673985 GCAGGGGGTTTCACTTTCAC 59.326 55.000 0.00 0.00 0.00 3.18
371 398 0.469144 GGCAGGGGGTTTCACTTTCA 60.469 55.000 0.00 0.00 0.00 2.69
372 399 0.469144 TGGCAGGGGGTTTCACTTTC 60.469 55.000 0.00 0.00 0.00 2.62
373 400 0.469892 CTGGCAGGGGGTTTCACTTT 60.470 55.000 6.61 0.00 0.00 2.66
374 401 1.153756 CTGGCAGGGGGTTTCACTT 59.846 57.895 6.61 0.00 0.00 3.16
422 450 3.376546 GGAGAGCAGAGCAATTACCAAAG 59.623 47.826 0.00 0.00 0.00 2.77
464 492 2.403561 AGGATCACCTCCCTTTCTAGC 58.596 52.381 0.00 0.00 46.27 3.42
529 564 3.956199 CGGTTGGTAGGTAGGTTCAGATA 59.044 47.826 0.00 0.00 0.00 1.98
536 575 1.004277 TCGTACGGTTGGTAGGTAGGT 59.996 52.381 16.52 0.00 38.02 3.08
537 576 1.750193 TCGTACGGTTGGTAGGTAGG 58.250 55.000 16.52 0.00 38.02 3.18
538 577 2.487762 TGTTCGTACGGTTGGTAGGTAG 59.512 50.000 16.52 0.00 38.02 3.18
539 578 2.487762 CTGTTCGTACGGTTGGTAGGTA 59.512 50.000 16.52 0.00 38.02 3.08
575 614 3.443145 ACACGGTGAATAAATCCCCAA 57.557 42.857 16.29 0.00 0.00 4.12
576 615 4.781775 ATACACGGTGAATAAATCCCCA 57.218 40.909 16.29 0.00 0.00 4.96
597 636 9.866655 AAGGAAGCCAAATGTATCATAAATCTA 57.133 29.630 0.00 0.00 0.00 1.98
601 640 6.572519 GCAAGGAAGCCAAATGTATCATAAA 58.427 36.000 0.00 0.00 0.00 1.40
630 670 2.009774 GGACGGGATTGATGAACACAG 58.990 52.381 0.00 0.00 0.00 3.66
639 679 1.382695 GGGAGAGGGACGGGATTGA 60.383 63.158 0.00 0.00 0.00 2.57
680 720 7.937394 GGCAAGGAGGTACAGTATTATATTGTT 59.063 37.037 5.73 0.00 30.84 2.83
696 736 0.839853 AAGAGAGCAGGCAAGGAGGT 60.840 55.000 0.00 0.00 0.00 3.85
712 752 5.048504 GGATGAAGATGAACACAAGCAAAGA 60.049 40.000 0.00 0.00 0.00 2.52
746 791 2.293122 CGATCTAGAAGCAGAGGGTGAG 59.707 54.545 0.00 0.00 0.00 3.51
748 793 2.028130 ACGATCTAGAAGCAGAGGGTG 58.972 52.381 0.00 0.00 0.00 4.61
749 794 2.028130 CACGATCTAGAAGCAGAGGGT 58.972 52.381 0.00 0.00 0.00 4.34
750 795 1.269517 GCACGATCTAGAAGCAGAGGG 60.270 57.143 0.00 0.00 0.00 4.30
812 877 2.203625 GCCAGGCCCCAAGTCAAA 60.204 61.111 0.00 0.00 0.00 2.69
845 910 9.444600 GAACTGGTATTTGGTAGTAAAGAATGA 57.555 33.333 0.00 0.00 0.00 2.57
1152 1249 3.083997 ATGGAGCCGGTGAGGTCC 61.084 66.667 1.90 1.47 43.70 4.46
1320 1417 4.143333 TAGACGCAGCCGAAGCCC 62.143 66.667 0.00 0.00 41.25 5.19
1835 2394 6.849502 TCTTCAGTTCAATTCATTCAGATGC 58.150 36.000 0.00 0.00 33.14 3.91
1938 2587 4.492646 TCCAGTCCTCATCCAGCAATATA 58.507 43.478 0.00 0.00 0.00 0.86
1941 2590 1.588239 TCCAGTCCTCATCCAGCAAT 58.412 50.000 0.00 0.00 0.00 3.56
1942 2591 1.003580 GTTCCAGTCCTCATCCAGCAA 59.996 52.381 0.00 0.00 0.00 3.91
1968 2617 0.036952 CCATGCCGAAGTCTGACAGT 60.037 55.000 10.88 0.00 0.00 3.55
2134 3691 9.468532 CCACCTACACATATATCAATATCATCG 57.531 37.037 0.00 0.00 0.00 3.84
2147 3704 2.999331 GTGCCAACCACCTACACATAT 58.001 47.619 0.00 0.00 38.55 1.78
2654 4738 2.102084 GCCTCAGTATCAGCACATGAGA 59.898 50.000 0.00 0.00 42.53 3.27
2668 4752 6.711277 TCACATGAATTAAACTAGCCTCAGT 58.289 36.000 0.00 0.00 0.00 3.41
2688 4772 5.750524 TCCCCGAAAATCTAATCAATCACA 58.249 37.500 0.00 0.00 0.00 3.58
2706 4790 4.675038 ACTAGGATTAACTAGGATCCCCG 58.325 47.826 8.55 1.77 43.72 5.73
2707 4791 5.651576 CGTACTAGGATTAACTAGGATCCCC 59.348 48.000 8.55 0.00 43.72 4.81
2708 4792 5.651576 CCGTACTAGGATTAACTAGGATCCC 59.348 48.000 8.55 0.00 43.72 3.85
2717 7081 6.016443 AGACATACTGCCGTACTAGGATTAAC 60.016 42.308 0.00 0.00 0.00 2.01
2741 7105 2.355756 CTCAGAACAACACCACCAACAG 59.644 50.000 0.00 0.00 0.00 3.16
2757 7121 2.419159 CGGCTGGAATTGATCACTCAGA 60.419 50.000 14.27 0.00 31.68 3.27
2758 7122 1.938577 CGGCTGGAATTGATCACTCAG 59.061 52.381 0.00 2.30 31.68 3.35
2775 7139 2.035961 TGCATACTATGACTCTTCCGGC 59.964 50.000 0.00 0.00 0.00 6.13
2777 7141 4.202060 ACACTGCATACTATGACTCTTCCG 60.202 45.833 0.00 0.00 0.00 4.30
2792 7156 2.585330 TCCACACAATTGACACTGCAT 58.415 42.857 13.59 0.00 0.00 3.96
2799 7163 6.432162 AGCCATATCATATCCACACAATTGAC 59.568 38.462 13.59 0.00 0.00 3.18
2800 7164 6.545567 AGCCATATCATATCCACACAATTGA 58.454 36.000 13.59 0.00 0.00 2.57
2844 7210 2.586635 GACGGGTGTGACAACGCA 60.587 61.111 10.26 0.00 38.63 5.24
2851 7217 0.762418 ACAGAAATGGACGGGTGTGA 59.238 50.000 0.00 0.00 0.00 3.58
2853 7219 0.762418 TCACAGAAATGGACGGGTGT 59.238 50.000 0.00 0.00 0.00 4.16
2855 7221 2.105821 TCTTTCACAGAAATGGACGGGT 59.894 45.455 0.00 0.00 0.00 5.28
2867 7233 3.248602 CCCTTTCGACAGTTCTTTCACAG 59.751 47.826 0.00 0.00 0.00 3.66
2926 7292 2.256591 AACTGCAGCTGCCGACTTG 61.257 57.895 34.64 18.95 41.18 3.16
2941 7307 1.961793 TTCGCTAAGTTGCCACAACT 58.038 45.000 7.15 7.15 0.00 3.16
3185 7570 9.872721 TGTAATTAACAACTGTTCGTATATGGA 57.127 29.630 0.00 0.00 39.31 3.41
3201 7588 9.868277 GAATTCATGACCCATTTGTAATTAACA 57.132 29.630 0.00 0.00 35.88 2.41
3211 7598 5.253330 ACTACGTGAATTCATGACCCATTT 58.747 37.500 29.89 11.36 36.72 2.32
3228 7615 6.643770 ACGAATTTAGTGTTGATGAACTACGT 59.356 34.615 0.00 0.00 32.79 3.57
3262 7650 8.244802 TCTAAATTCAAAACACGACCTGAAAAA 58.755 29.630 0.00 0.00 31.94 1.94
3272 7660 7.621832 TCTGCAAATCTAAATTCAAAACACG 57.378 32.000 0.00 0.00 0.00 4.49
3404 7795 3.568430 GGCCCTGCATATACTTTGGTAAC 59.432 47.826 0.00 0.00 0.00 2.50
3414 7805 1.915489 CATACCCTGGCCCTGCATATA 59.085 52.381 0.00 0.00 0.00 0.86
3415 7806 0.700564 CATACCCTGGCCCTGCATAT 59.299 55.000 0.00 0.00 0.00 1.78
3446 7839 4.465632 TCGCTACTGCCTTTCTTAATCA 57.534 40.909 0.00 0.00 35.36 2.57
3462 7855 3.994392 GGTGAACTCTTGACATTTCGCTA 59.006 43.478 0.00 0.00 0.00 4.26
3494 7887 4.771684 GCAAGCTATGTTGCGTGG 57.228 55.556 4.83 0.00 43.24 4.94
3519 7916 9.913310 ATGTCTAATCGATATAGAAGATCCTGA 57.087 33.333 14.73 0.00 31.52 3.86
3588 7985 6.653020 TCCTGCATGAGTTTCACTACATATT 58.347 36.000 0.00 0.00 0.00 1.28
3590 7987 5.187772 ACTCCTGCATGAGTTTCACTACATA 59.812 40.000 17.79 0.00 42.92 2.29
3591 7988 4.019860 ACTCCTGCATGAGTTTCACTACAT 60.020 41.667 17.79 0.00 42.92 2.29
3592 7989 3.324846 ACTCCTGCATGAGTTTCACTACA 59.675 43.478 17.79 0.00 42.92 2.74
3593 7990 3.929610 GACTCCTGCATGAGTTTCACTAC 59.070 47.826 23.19 7.39 45.41 2.73
3594 7991 3.055819 GGACTCCTGCATGAGTTTCACTA 60.056 47.826 23.19 0.00 45.41 2.74
3595 7992 2.289945 GGACTCCTGCATGAGTTTCACT 60.290 50.000 23.19 1.97 45.41 3.41
3596 7993 2.079925 GGACTCCTGCATGAGTTTCAC 58.920 52.381 23.19 11.86 45.41 3.18
3597 7994 1.699083 TGGACTCCTGCATGAGTTTCA 59.301 47.619 23.19 20.22 45.41 2.69
3598 7995 2.479566 TGGACTCCTGCATGAGTTTC 57.520 50.000 23.19 18.33 45.41 2.78
3599 7996 4.785346 ATATGGACTCCTGCATGAGTTT 57.215 40.909 23.19 14.51 45.41 2.66
3600 7997 5.802465 CATATATGGACTCCTGCATGAGTT 58.198 41.667 23.19 11.97 45.41 3.01
3619 8016 7.176515 TGGGCGAACTCATTATATTTTGCATAT 59.823 33.333 0.00 0.00 31.01 1.78
3631 8028 2.682856 GCTCATTTGGGCGAACTCATTA 59.317 45.455 0.00 0.00 0.00 1.90
3640 8037 3.814268 CCGGTGCTCATTTGGGCG 61.814 66.667 0.00 0.00 0.00 6.13


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.